As I have started playing this game again I was wondering, how many important choices are the in the game? I'm talking about choices like;

Joining the Stormcloaks or Imperials and fight the war.
Make peace through diplomacy siding with the Stormcloaks or Imperials.
Killing the emperor/destroying the Dark Brotherhood
Choosing standing stone
Choosing Fus, Feim or Yol from Paarthurnax
Kill or leave Paarthurnax alone

Are there more choices likes these?

There aren't really many game-changing choices, at least that I know of. It always comes down to something similar.
P.S. The Shout for Paarthy's meditation can be changed infinite times. Standing Stones, too.

Choosing how to play most of the Daedric Questlines.
Aiding a Redgaurd, or letting her get captured.
Choosing to never smell like a wet dog and have hair growing out of your ears, or not be able to finish completing the Companions questline.

These are the ones I can think of as significant:
-Empire or Stormcloaks? This affects who the Jarl is in several holds.
-For that matter, Civil War or no? This affects Whiterun specifically.
-Join or destroy the Dark Brotherhood?
-Help the Silverbloods, or the Forsworn, in Markarth? Could remove several merchants and other non-essential NPCs.
-Paarthurnax or the Blades? Later in the game.

Should I go left or should I go right. Very important when you come to a fork in the road.

All of these choices seem important now, but something must be about to happen that will completely overshadow all of these events. How else is Bethesda going to explain the huge difference in outcome that these choices have in the next game?

Perhaps Alduin wasn't actually slain and he'll come back to eat the world in the expansion, forcing time to start over again. Then the next game could be at the during the Dawn era or something cool like that. I've always wanted to play a game from the earlier eras...

Hard to tell if that is sarcasm or not. Nothing you did in MW mattered in OB and nothing you did in OB mattered in Skyrim. I am also quite positive that nothing you do in Skyrim will effect the next game. This isn't Mass Effect.

To be honest OP there are no choices that really ruin anything. The above posters have listed some things that perminately change things in the game, but none of those things really matter.

Azura's star or black Azura's star.
Werewolf or cure.
Vampire or not
Married or single (and who to marry)

Probably the biggest choices are dragons or no dragons and traditional or same-six marriage.
Dragons or no dragons for sure. Entirely different game if you don't panic everytime a shadow goes overhead.

Every choice made at the end of one of the games is at the very least referred to at some point during the next game. For example, in Daggerfall, there are six possible endings that the player could choose, so Bethesda had to come up with a way to explain this. They said that the activation of the Numidium caused a "Dragon Break" (basically a period where time ceases to exist and many strange things can happen that don't when time is flowing normally), which allowed all six of the endings to occur at the same time.

So, basically, if they plan on having another TES game, they'll explain how all of the choices made in Skyrim (such as which side on the civil war, whether to kill the DB or not {which leads to the Emperor being assassinated}, whether or not to kill Paarthurnax, etc) and their hugely different outcomes will all work out. Right now my two main guesses would be that either the player using the Elder Scroll and going back in time to learn Dragonrend caused another Dragon Break, which allows all of these things to occur at the same time, or what I said above; Alduin comes back, eats the world, and time starts over again.

Start the MQ or not?
I vote not.

Kill Cicero or not?
Who to sacrifice for boeathia(daedric prince)

Not my choice, the developers choice. My choices make no difference at all for the next game. There is no Save Game File data being used to determine the story in the next game. The MQ in whatever game you are playing is considered as being done in the next game. It would be interesting to see the Civil War affect the next game, but I'm sure the developers will decide who won and that will be what's written in the next games new history books. IMO the 'cannon' story will be the Stormcloaks won, but I'll leave that for another thread.

I'm just curious to see how Bethesda is going to explain the different outcomes from different choices the player could make throughout the game. They won't just decide who won and force it to come out that way. Why would they give players the choice in the first place if they were just going to decide for you in the long run? Like I've been saying; I think some large event is going to happen that either allows both choices to happen at the same time (a Dragon Break) or an event that is so huge and overshadowing that it's almost as if the whole civil war never happened (like Alduin returning to eat the world).

This your first TES game? Beth does exactly that. Never addresses the different choices a player can make for a toon. The devs decide the outcome, and refer to it only marginally in the next game. Those of us who've played since the beginning know how it will be next time: the Dragonborn will be said to have done whatever it took to implement the devs' decision regarding the MQ, the Civil War, perhaps the TG and DB (though likely not).

No, it's not. And you're wrong. I gave an example above, and that's not the only one there is. In every TES game, there is at least some sort of reference to what's happened in the previous games. They will explain how these events worked out if they make another game. They might not do it directly, but it'll be in a book somewhere or some NPC will talk about it in some way.

Besides, when's the last time the player has had a choice like the civil war choice that has such a huge difference in outcome? If the player sides with the Stormcloaks, the Thalmor has a much clearer path to their goal. If the player sides with the Empire, there's still some hope that they could pull together and win the fight.

That's what I said: "....the Dragonborn will be said to have done whatever it took to implement the devs' decision regarding the MQ, the Civil War, perhaps the TG and DB (though likely not)."

I know exactly how it works. I've played every TES game beginning with Arena. They don't explain anything about the different choices a player can make - they have an outcome set, and that's how it is. I figure they've had the outcome for every game they ever plan to make set in stone since Arena was in beta, or even before. And yes, usually it's in a book or books in the game itself, though in previous games I've run across NPCs who mention bits of "recorded history" regarding the previous game, it's outcome, and its hero.

Hopefully the devs decide that the Empire won the civil war. If not then Skyrim will be ruled by the Thalmor in the future...and that will not be cool at all.

Well.... that would depend on if the next game involves "doing something" about the Thalmor. I can see that happening.... though the one thing I can say about the TES devs is that they are VERY close-mouthed about "the next game" and what it involves - until they actually are into the development cycle.

If they don't explain the different choices players make, then why did they bother to do so with Daggerfall? They could have just chosen one ending and went with it, but they decided to say that activating the Numidium caused a Dragon Break and allowed all of the possible outcomes from Daggerfall to occur at the same time.

You didn't answer my question from my last post -- besides Daggerfall, when's the last time the player has had a choice that actually mattered in the outcome of the series? Most choices that they give are just a means to an end and the end (except Daggerfall) is always the same, regardless of how you got there. That's not the case here. Choosing either the Empire or the Stormcloaks appears to have very different outcomes at this point.

Yeah, they did that once, don't see them doing it again. Mostly it was a "nothing" deal anyway.... by the time Morrowind came out, did you even remember what you'd done in Daggerfall or Arena? If there's 6 years or so between games, who keeps track?

I don't honestly care what they do. Since I can't "move" my toons to the next game, nothing matters. *shrug* If I could keep one toon through the entire series, THEN things would matter.

Whether to kill Nilsine Shattershield or not.
Seriously, that's one example of serious consequences in Skyrim!

Why do you keep saying that something done in Daggerfall mattered in Morrowind? Nothing I did in Daggerfall changed Morrowind at all. I played Daggerfall to death, but nothing I, me, myself, did in Daggerfall was reflected in MW or any other game. Like always the events of the prior games are mentioned as history in the latest games. There are not different versions of the TES books in my MW game because of something I did in Daggerfall. The Developers decide what happened.

Concerning the Civil War, following the other factions quests it is pretty apparent that the Empire is finished and Skyrim is showing us the end of the dynasty. Even if they somehow won the war in Skyrim they have been destroyed from within. Mankinds only hope is if the Stormcloaks win and then rally support against the DA.

there are no choices that make a major difference in the end, they all got pretty much the same outcome anyway